This starts at the main mission "Humanitarian Aid". In this mission you'll meet the ally for the entire trophy.
To progress you need to complete the next main mission and you'll recieve a call from MJ asking for Spidey to investigate an underground base. Three bases also spawn in Chinatown, Greenwich and Midtown.
side note
Midtown's base is also a perfect candidate for the 100 hit combo if you're still struggling, the enemies are easy enough using electric webs and web bombs to disable them enough to achieve the streak required for the token (95) which only leaves 5 to get for the trophy.
Once they are all completed, you'll eventually recieve a call from your ally and the side mission Aiding a human will spawn, it's a simple mission that's basiccaly the same as any random crime in free roam. Trophy pops after a cutscene.